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Assarsson M, Söderman J, Seifert O. Significant Correlation Between Cutaneous Abundance of Streptococcus and Psoriasis Severity in Patients with FBXL19 Gene Variants. Acta Derm Venereol 2024; 104:adv34892. [PMID: 38898675 DOI: 10.2340/actadv.v104.34892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Psoriasis results from both genetic predisposition and environmental triggers, such as Streptococcal infections. This study aimed to explore the correlation between the abundance of the Streptococcus genus on the skin and psoriasis severity in individuals carrying specific psoriasis-associated genetic variants. Studying 39 chronic plaque psoriasis patients, the elbow skin microbiome and 49 psoriasis-related single nucleotide polymorphisms (SNPs) were analysed using a MiSeq instrument for 16S rDNA sequencing, and CLC Genomic Workbench for processing and analysis. Through multivariate linear regression analysis, a positive correlation was found between Streptococcus genus abundance and psoriasis severity in patients with certain FBXL19 gene-related heterozygous SNPs (rs12924903, rs10782001, rs12445568). Conversely, a negative association was observed in patients with homozygous genotypes. Moreover, we identified an association between Streptococcus abundance and psoriasis severity in patients with genetic variants related to IL-22, ERAP1, NOS2, and ILF3. This is the first study highlighting a positive association between Streptococcus skin colonization and psoriasis severity in patients with heterozygous genotypes within the FBXL19 gene region. FXBL19 targets the IL-33/IL1RL1 axis, crucial in infectious diseases and innate immunity promotion. These novel results suggests an intricate interaction among host genetics, Streptococcus skin colonization, and psoriasis inflammation, offering potential avenues for novel treatment approaches.
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Affiliation(s)
- Malin Assarsson
- Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; Division of Dermatology and Venereology, Region Jönköping County, Jönköping, Sweden.
| | - Jan Söderman
- Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; Laboratory Medicine, Region Jönköping County, Jönköping, Sweden
| | - Oliver Seifert
- Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; Division of Dermatology and Venereology, Region Jönköping County, Jönköping, Sweden
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Bui A, Kumar S, Liu J, Orcales F, Gulliver S, Tsoi LC, Gulliver W, Liao W. A partitioned 88-loci psoriasis genetic risk score reveals HLA and non-HLA contributions to clinical phenotypes in a Newfoundland psoriasis cohort. Front Genet 2023; 14:1141010. [PMID: 37323656 PMCID: PMC10265743 DOI: 10.3389/fgene.2023.1141010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Psoriasis is an immune-mediated inflammatory skin disease typically characterized by erythematous and scaly plaques. It affects 3% of the Newfoundland population while only affecting 1.7% of the general Canadian population. Recent genome-wide association studies (GWAS) in psoriasis have identified more than 63 genetic susceptibility loci that individually have modest effects. Prior studies have shown that a genetic risk score (GRS) combining multiple loci can improve psoriasis disease prediction. However, these prior GRS studies have not fully explored the association of GRS with patient clinical characteristics. In this study, we calculated three types of GRS: one using all known GWAS SNPs (GRS-ALL), one using a subset of SNPs from the HLA region (GRS-HLA), and the last using non-HLA SNPs (GRS-noHLA). We examined the relationship between these GRS and a number of psoriasis features within a well characterized Newfoundland psoriasis cohort. We found that both GRS-ALL and GRS-HLA were significantly associated with early age of psoriasis onset, psoriasis severity, first presentation of psoriasis at the elbow or knee, and the total number of body locations affected, while only GRS-ALL was associated with a positive family history of psoriasis. GRS-noHLA was uniquely associated with genital psoriasis. These findings clarify the relationship of the HLA and non-HLA components of GRS with important clinical features of psoriasis.
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Affiliation(s)
- Audrey Bui
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
- Lake Erie College of Osteopathic Medicine, Bradenton, FL, United States
| | - Sugandh Kumar
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
| | - Jared Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
| | - Faye Orcales
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
| | | | - Lam C. Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States
| | - Wayne Gulliver
- NewLab Clinical Research Inc, St. John’s, NL, Canada
- Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, CA, United States
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Tawfik NZ, Abdallah HY, Hassan R, Hosny A, Ghanem DE, Adel A, Atwa MA. PSORS1 Locus Genotyping Profile in Psoriasis: A Pilot Case-Control Study. Diagnostics (Basel) 2022; 12:diagnostics12051035. [PMID: 35626191 PMCID: PMC9139320 DOI: 10.3390/diagnostics12051035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: The psoriasis susceptibility 1 (PSORS1) locus, located within the major histocompatibility complex, is one of the main genetic determinants for psoriasis, the genotyping profile for three single-nucleotide polymorphisms (SNPs) comprising the PSORS1 locus: rs1062470 within PSORS1C1/CDSN genes, rs887466 within PSORS1C3 gene, rs10484554 within LOC105375015 gene, were investigated and correlated with psoriasis risk and severity. (2) Methods: This pilot case-controlled study involved 100 psoriatic patients and 100 healthy individuals. We investigated three SNPs and assessed the relative gene expression profile for the PSORS1C1 gene. We then correlated the results with both disease risk and severity. (3) Results: The most significantly associated SNP in PSORS1 locus with psoriasis was rs10484554 with its C/T genotype 5.63 times more likely to develop psoriasis under codominant comparison. Furthermore, C/T and T/T genotypes were 5 times more likely to develop psoriasis. The T allele was 3 times more likely to develop psoriasis under allelic comparison. The relative gene expression of PSORS1C1 for psoriatic patients showed to be under-expressed compared to normal controls. (4) Conclusions: Our study revealed the association of the three studied SNPs with psoriasis risk and severity in an Egyptian cohort, indicating that rs10484554 could be the major key player in the PSORS1 locus.
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Affiliation(s)
- Noha Z. Tawfik
- Dermatology, Venereology and Andrology Department, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Correspondence: ; Tel.: +20-127-4504926
| | - Hoda Y. Abdallah
- Medical Genetics Unit, Histology & Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ranya Hassan
- Clinical Pathology Department, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Alaa Hosny
- Ministry of Health, Cairo 11435, Egypt; (A.H.); (D.E.G.); (A.A.)
| | - Dina E. Ghanem
- Ministry of Health, Cairo 11435, Egypt; (A.H.); (D.E.G.); (A.A.)
| | - Aya Adel
- Ministry of Health, Cairo 11435, Egypt; (A.H.); (D.E.G.); (A.A.)
| | - Mona A. Atwa
- Dermatology, Venereology and Andrology Department, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
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Guo Y, Cheng H, Yuan Z, Liang Z, Wang Y, Du D. Testing Gene-Gene Interactions Based on a Neighborhood Perspective in Genome-wide Association Studies. Front Genet 2021; 12:801261. [PMID: 34956337 PMCID: PMC8693929 DOI: 10.3389/fgene.2021.801261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Unexplained genetic variation that causes complex diseases is often induced by gene-gene interactions (GGIs). Gene-based methods are one of the current statistical methodologies for discovering GGIs in case-control genome-wide association studies that are not only powerful statistically, but also interpretable biologically. However, most approaches include assumptions about the form of GGIs, which results in poor statistical performance. As a result, we propose gene-based testing based on the maximal neighborhood coefficient (MNC) called gene-based gene-gene interaction through a maximal neighborhood coefficient (GBMNC). MNC is a metric for capturing a wide range of relationships between two random vectors with arbitrary, but not necessarily equal, dimensions. We established a statistic that leverages the difference in MNC in case and in control samples as an indication of the existence of GGIs, based on the assumption that the joint distribution of two genes in cases and controls should not be substantially different if there is no interaction between them. We then used a permutation-based statistical test to evaluate this statistic and calculate a statistical p-value to represent the significance of the interaction. Experimental results using both simulation and real data showed that our approach outperformed earlier methods for detecting GGIs.
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Affiliation(s)
- Yingjie Guo
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Honghong Cheng
- School of Information, Shanxi University of Finance and Economics, Taiyuan, China
| | - Zhian Yuan
- Research Institute of Big Data Science and Industry, Shanxi University, Taiyuan, China
| | - Zhen Liang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yang Wang
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Debing Du
- Beidahuang Industry Group General Hospital, Harbin, China
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